RII Track-2 FEC: Building Field-Based Ecophysiological Genome-to-Phenome Prediction

RII Track-2 FEC：构建基于现场的生态生理基因组到现象组预测

• 批准号: 1826820
• 负责人: Stephen Welch
• 金额: $ 400万
• 依托单位: Kansas State University
• 依托单位国家: 美国
• 项目类别: Cooperative Agreement
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-08-15 至 2023-07-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1826820&HistoricalAwards=false
• 关键词: RII; Track; FEC; Building; Field

Nontechnical Description:It is widely agreed that agricultural crop production is not growing to meet the needs of the increasing human population. This project brings together researchers from the Kansas State University, Oklahoma State University, and Langston University (a Historically Black University), to develop a new way to model and predict important crop production traits in wheat. One of the greatest challenges of current crop trait prediction is that it falls in an underpopulated borderland between plant physiology, biological engineering, genetics, computational biology, mathematics, statistics, and computer science. Therefore, to bridge this gap, mathematical models will be produced that combine both observational data using Unmanned Aerial Vehicles and robots, and genetics data. These new models are expected to simplify crop modeling for farmers, and will aid in farm management, and can easily be applied to other crops and in other environments. Many additional benefits will also accrue. First, commonalities between these mathematical models will mean that results will readily transfer to many other crops. Moreover, the benefits of combining genetic and observational data in this way to predict crop traits will aid on-farm crop management, enhancing food security. Educational programs for undergraduates, graduate students, and faculty in these disciplines will enlarge a globally competitive workforce. Involvement of key corporate partners will also speed research transfer to the private sector both directly and by creating a market for project trainees. Finally, the sensing/measuring devices to be bought or built will enhance the ability of partners to conduct a wide range of related, data-intensive research. Technical Description:It is widely agreed that agricultural crop production is not on track to meet the production doubling needed by 2050 for humanity to avoid major food security disruption. Farmers need genetically-informed analytics to predict the outcomes of management options amongst which they may choose and apply in their unique field environments. This project brings together researchers from the sity of Kansas State University, Oklahoma State University, and Langston University (a Historically Black University), and presents new genetically- and physiologically-informed proof-of-concept wheat physiologically-based crop models (CMs). These CMs will link to state-of-the-art field monitoring technologies with genomic data, thus rebalancing direct monitoring vs. indirect model calculation. The data will include: (1) airborne imagery to extract morphological features, canopy temperatures, and light interception. (2) Multivariate soil profile data will be collected by robots at 2-30 cm (horizontal/vertical) and three-day temporal resolution. (3) Gene expression data on selected double haploid lines over 64 combinations of locations, dates, and years will aid in model building. (4) CM and quantitative genetics integration will also be aided by expanding the number of genotyped wheat lines within the Kansas and Oklahoma breeding programs. Such large data sets ordinarily pose computational challenges for models as complex as CMs. In contrast to extant CMs, the new models will efficiently combine differential equation solvers, maximum entropy and Bayesian methods, and high-performance computing. The results will be methods able to predict the traits of novel genotypes in novel environments not used to construct the models. Many additional benefits will also accrue. First, commonalities between CMs will mean that results will readily transfer to many other crops. Moreover, increased genome to phenome prediction accuracy will aid on-farm crop management, enhancing food security. Educational programs for undergraduates, graduate students, and faculty in these disciplines will create and enlarge a globally competitive workforce. Involving key corporate partners will also speed research transfer directly and by creating a market for project trainees. Finally, the sensing/measuring devices to be bought or built will enhance partner ability to conduct a wide range of related, data-intensive research.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

非技术性描述：人们普遍认为，农作物产量的增长不能满足不断增长的人口的需求。 该项目汇集了来自堪萨斯州立大学、俄克拉荷马州州立大学和兰斯顿大学（一所历史上的黑人大学）的研究人员，以开发一种新的方法来建模和预测小麦的重要作物生产性状。 当前作物性状预测面临的最大挑战之一是，它福尔斯处于植物生理学、生物工程、遗传学、计算生物学、数学、统计学和计算机科学之间的边缘地带。因此，为了弥合这一差距，将建立数学模型，将联合收割机使用无人机和机器人的观测数据与遗传学数据结合起来。 这些新模型有望简化农民的作物建模，有助于农场管理，并可轻松应用于其他作物和其他环境。 许多额外的好处也将随之而来。 首先，这些数学模型之间的共性将意味着结果将很容易转移到许多其他作物。此外，以这种方式结合遗传和观测数据来预测作物性状的好处将有助于农田作物管理，提高粮食安全。 针对这些学科的本科生、研究生和教师的教育计划将扩大具有全球竞争力的劳动力队伍。主要公司伙伴的参与也将直接或通过为项目受训人员创造市场，加速研究成果向私营部门的转移。 最后，购买或建造的传感/测量设备将增强合作伙伴进行广泛相关的数据密集型研究的能力。人们普遍认为，农业作物生产无法实现到2050年人类避免粮食安全受到重大破坏所需的产量翻一番。农民需要遗传信息分析来预测管理选项的结果，他们可以在其中选择并应用于其独特的田间环境。该项目汇集了来自堪萨斯州立大学、俄克拉荷马州州立大学和兰斯顿大学（一所历史上的黑人大学）的研究人员，并提出了新的遗传和生理信息的概念验证小麦生理作物模型（CM）。 这些CM将通过基因组数据与最先进的现场监测技术相连接，从而重新平衡直接监测与间接模型计算。 数据将包括：（1）机载图像，以提取形态特征，冠层温度和光截获。(2)多变量土壤剖面数据将由机器人以2-30厘米（水平/垂直）和三天时间分辨率收集。 (3)在64个地点、日期和年份的组合上选择的双单倍体品系的基因表达数据将有助于模型的建立。(4)在堪萨斯和俄克拉荷马州的育种计划中，还将通过扩大基因型小麦品系的数量来帮助CM和数量遗传学的整合。 如此大的数据集通常会对像CM这样复杂的模型提出计算挑战。 与现有的CM相比，新模型将有效地结合联合收割机微分方程求解器，最大熵和贝叶斯方法，以及高性能计算。 这些结果将是能够在新环境中预测新基因型性状的方法，而不是用于构建模型。许多额外的好处也将随之而来。 第一，CM之间的共性将意味着结果将很容易转移到许多其他作物。此外，提高基因组对表型组的预测准确性将有助于农田作物管理，提高粮食安全。 这些学科的本科生、研究生和教师的教育计划将创造和扩大具有全球竞争力的劳动力。让主要的企业伙伴参与进来，也将直接加快研究成果的转让，并为项目受训人员创造一个市场。 最后，购买或建造的传感/测量设备将提高合作伙伴进行广泛的相关数据密集型研究的能力。该奖项反映了NSF的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

项目成果

Chapter One - The role of artificial intelligence in crop improvement

第一章——人工智能在作物改良中的作用

• 发表时间: 2024
• 期刊: Advances in Agronomy
• 作者: Negus, K;Welch S;Yu, J.
• 通讯作者: Yu, J.

Predictive Characterization for Seed Morphometric Traits for Genebank Accessions Using Genomic Selection

• DOI: 10.3389/fevo.2020.00032
• 发表时间: 2020-03-17
• 期刊: FRONTIERS IN ECOLOGY AND EVOLUTION
• 影响因子: 3
• 作者: Kehel, Zakaria;Sanchez-Garcia, Miguel;Amril, Ahmed
• 通讯作者: Amril, Ahmed

A hierarchical Bayesian approach to dynamic ordinary differential equations modeling for repeated measures data on wheat growth

小麦生长重复测量数据动态常微分方程建模的分层贝叶斯方法

• DOI: 10.1016/j.fcr.2022.108549
• 发表时间: 2022
• 期刊: Field Crops Research
• 影响因子: 5.8
• 作者: Poudel, Pratishtha;Bello, Nora M.;Lollato, Romulo P.;Alderman, Phillip D.
• 通讯作者: Alderman, Phillip D.

Ecophysiological modeling of yield and yield components in winter wheat using hierarchical Bayesian analysis

使用分层贝叶斯分析建立冬小麦产量和产量组成部分的生态生理模型

• DOI: 10.1002/csc2.20652
• 发表时间: 2022
• 期刊: Crop Science
• 影响因子: 2.3
• 作者: Poudel, Pratishtha;Bello, Nora M.;Marburger, David A.;Carver, Brett F.;Liang, Ye;Alderman, Phillip D.
• 通讯作者: Alderman, Phillip D.

A Spatial AI-Based Agricultural Robotic Platform for Wheat Detection and Collision Avoidance

• DOI: 10.3390/ai3030042
• 发表时间: 2022-08
• 期刊: AI
• 作者: Sujith Gunturu;Arslan Munir;Hayat Ullah;S. Welch;D. Flippo